Genetically Encoded Stimuli-Responsive Cytoprotective Hydrogel Capsules for Single Cells Provide Novel Genotype–Phenotype Linkage

Modification of cell surfaces with synthetic polymers is a promising approach for regulating cellular behavior. Here, we describe a genetically controlled strategy for selectively encapsulating single yeast cells in synthetic microniches comprising cross-linked phenol-modified alginate and chitosan hydrogel capsules. Our system links inducible gene expression with enzyme-mediated hydrogel polymerization and provides a novel genotype–phenotype linkage whereby only cells carrying a requisite gene encoding a flavin adenine dinucleotide-dependent oxidoreductase undergo autonomous enzyme-mediated surface polymerization, resulting in the formation of hydrogel capsules. The composition of the hydrogel capsules is highly tunable and the capsule sizes are pH-responsive, allowing for control of capsule porosity and shell diameters over a range of 15–80 μm. The hydrogel capsules prevent extracellular proteins from reaching the cell surface, thereby conferring cellular immunity to lytic enzyme cocktails and rendering the hydrogel capsules cytoprotective against osmotic shock. We demonstrate the utility of this genetically controlled artificial hydrogel-encapsulated cell phenotype by isolating and enriching uniform eukaryotic cell lineages from genetically heterogeneous cell mixtures at 95–100% efficiency. The encapsulated cells remained viable and were capable of dividing and breaking free from their hydrogel capsules, allowing further propagation of selected cells. Our bottom-up approach to cellular compartmentalization links inducible intracellular genetic components with an artificial extracellular matrix that resists enzymatic lysis and mediates communication with the surrounding environment through a size-tunable and permeable hydrogel capsule.